siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass

Abstract

BackgroundUnderstanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes.ResultsWe performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar ‘Alamo’ using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development.ConclusionsThis study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1202-0) contains supplementary material, which is available to authorized users.

Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa and related species

“…In this study, we found a similar level of DNA methylation in regions encoding for lncRNA compared to previously described DNA methylation in the B. rapa genome [36]. Levels of DNA methylation can be positively regulated by siRNAs through the RdDM pathway [56], and Pol IV is important for biogenesis of 24-nt siRNAs [57].…”

Mutation of a major CG methylase alters genome-wide lncRNA expression in rice

“…This suggests that other unknown intrinsic features of En/Spm transposons and/or other regulatory process(es) involved in their de-repression must influence mutant-specific lncRNA expression after the null mutation of OsMET1-2 . In addition to the previously reported co-localization of TEs with expressed lncRNAs in rice and other plant species ( Wang et al 2017 a; Yan et al 2018 ), this study provides a clear example of the direct negative regulation of lncRNA expression by CG methylation of TEs in a monocot species.…”

“…The close association between transposable elements (TEs) and lncRNA expression has inspired a number of investigations into the regulation of lncRNA expression by DNA methylation ( Wang et al 2015 ; Yan et al 2018 ; Chen et al 2019 ). Most of these studies have characterized the DNA methylation (in CG, CHG, and CHH contexts) around genomic regions that generate lncRNAs and have reached a consistent conclusion: CG and CHG methylation tends to be negatively correlated with lncRNA expression ( Wang et al 2015 ; Xu et al 2018 ; Yan et al 2018 ). Notably, because no detailed analysis of DNA methylation mutants were involved, these previous studies are based on correlation analyses only and therefore do not reveal a causal relationship.…”

Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)

“…Using Bisulfite sequencing (BS-Seq) and Methylated DNA immunoprecipitation sequencing (MeDIP-Seq), similar DNA methylation patterns between AP13 and VS6 have been revealed, and the methylation levels were higher in Transposable elements (TEs) when compared to genic regions [23]. The recent bisulfite sequencing study suggested small interfering RNAs (siRNAs) positively regulate DNA methylation and thereby interferes with gene and long non-coding RNAs (lncRNAs) expression in switchgrass [24]. However, the genome-wide distribution of histone modifications in switchgrass has not been reported.…”